Onto-Tools protocols

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Onto-Tools specifications

Information


Unique identifier OMICS_26182
Name Onto-Tools
Alternative name ROnto Tools
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained No

Documentation


Maintainers


This tool is not maintained anymore.

Additional information


https://bioconductor.org/packages/release/bioc/vignettes/ROntoTools/inst/doc/rontotools.pdf

Information


Unique identifier OMICS_26182
Name Onto-Tools
Alternative name ROnto Tools
Software type Package/Module, Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 2.8.0
Stability Stable
Requirements
methods, BiocGenerics, RUnit, graph, Rgraphviz, KEGGgraph, boot, KEGGREST
Maintained Yes

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Documentation


Maintainers


  • person_outline Sorin Draghici <>
  • person_outline Calin Voichita <>

Additional information


https://bioconductor.org/packages/release/bioc/vignettes/ROntoTools/inst/doc/rontotools.pdf

Publication for Onto-Tools

Onto-Tools in pipeline

2012
PMCID: 3441782
PMID: 22494416
DOI: 10.1186/1475-2867-12-14

[…] the impact factor (if) analysis that considers exact fold changes of differentially expressed genes for generation of the corresponding kegg pathway was performed by using the pathway-express tool (onto-tools, intelligent systems and bioinformatics laboratory) []., ipa is a knowledgebase that contains approximately 2,500,000 biological and chemical interactions and functional annotations […]


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Onto-Tools in publications

 (51)
PMCID: 5908625
PMID: 29642183
DOI: 10.1097/MD.0000000000010362

[…] the cut-off criterion of p-value <.05 were chosen as degs., to explore what molecular functions changed in group s, go functional enrichment analysis of degs was performed by onto-express in onto-tools package (http://vortex.cs.wayne.edu/projects.html).[] the p-value <.05 was used as the cut-off criterion., to reveal the interactions of the screened degs, the search tool […]

PMCID: 5767188
PMID: 29375545
DOI: 10.3389/fimmu.2017.01792

[…] then analyzed by whole mouse genome 44k microarray kit (agilent technology cat no: g4122f, chip id no: 014868) various genes that were analyzed by pathway tools version 15.0, metacyc version 15.0. onto-tools pathway express was used to map differentially expressed genes, and gene spring 12.6.1 software (agilent technologies, santa clara, ca, usa) was used to prepare corresponding heat map. […]

PMCID: 5733474
PMID: 29321746
DOI: 10.3389/fpsyt.2017.00271

[…] (mathworks, natick, ma, usa) and (ii) an empirical bayes moderated t-test, implemented by limma package of bioconductor, an r-based open-source software ()., ingenuity pathway analysis (ipa) and onto-tools pathway-express software tools were applied. ipa determines the probability that a given gene set is associated with predefined pathways beyond what would be expected by random chance (). […]

PMCID: 5717999
PMID: 29225558
DOI: 10.1186/s12014-017-9175-8

[…] formalin-fixed and paraffin-embedded (ffpe) samples. proteins significantly altered in the metastatic lesions were associated with pathways linked to cancer progression using pathway-express (onto-tools) pathway analyses, providing important information about the progression of melanoma []. these examples highlight how identifying differential protein expression and altered molecular […]

PMCID: 5440822
PMID: 28508872
DOI: 10.1038/ncomms15237

[…] or batch effect for each gene independently. expression values were transformed in log2, and probesets were mapped using the entrez gene probeset definition. the pathway-express tool from the onto-tools (http://vortex.cs.wayne.edu) was used to assess biological processes and pathways affected at different stages of er+ breast tumour samples. genes encoding for human abps were selected […]


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Onto-Tools institution(s)
Department of Computer Science, Wayne State University, MI, USA; Department of Obstetrics and Gynecology, Karmanos Cancer Institute, Detroit, MI, USA; Department of Molecular Biology and Genetics, Karmanos Cancer Institute, Detroit, MI, USA
Onto-Tools funding source(s)
Supported by the NSF grant number NSF0234806, USMRMC grant number DAMD17-03-2-0035, NIH grant numbers RO1-NS045207-01 and R21-EB000990-01, and Michigan Life Sciences Corridor grant number MLSC-27.

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